schrodinger.application.glide.xpdes module¶
Classes for reading and writing Glide XP Descriptor blocks from pose files.
Copyright Schrodinger LLC. All rights reserved.
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schrodinger.application.glide.xpdes.
extract_Phob_pack_ligand_indices
(data_row)¶ Returns the ligand indices of the Phob_pack indices data row. The Phob_pack data block contains a row of indices containing [pack value, number of ligand indices, number of protein indices,
lig_0, lig_1, lig_2, …, prot_0, prot_1, prot_2, …]Note that indices in this data block are zero based, and are incremented here for use in ct atom index access.
Parameters: data_row (list of int) – second row in the Phob_pack data block Returns: ligand indices in the Phob_pack data block Return type: list of int
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schrodinger.application.glide.xpdes.
get_prop
(cthandle, dn)¶ Helper function for m_glide_XPviz_* functions
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schrodinger.application.glide.xpdes.
get_prop_idx
(cthandle, dn, dim)¶ Helper function for m_glide_XPviz_* functions
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schrodinger.application.glide.xpdes.
m_glide_XPviz_hbonds
(cthandle)¶
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schrodinger.application.glide.xpdes.
m_glide_XPviz_phobcon_hb
(cthandle)¶
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schrodinger.application.glide.xpdes.
m_glide_XPviz_hexsp
(cthandle)¶
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schrodinger.application.glide.xpdes.
m_glide_XPviz_phobpack
(cthandle)¶
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schrodinger.application.glide.xpdes.
m_glide_XPviz_stacking
(cthandle)¶
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schrodinger.application.glide.xpdes.
m_glide_XPviz_rotbonds
(cthandle)¶
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schrodinger.application.glide.xpdes.
m_glide_XPviz_watmol
(cthandle)¶
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schrodinger.application.glide.xpdes.
m_glide_XPviz_hexpairs
(cthandle)¶
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schrodinger.application.glide.xpdes.
m_glide_XPviz_exposure
(cthandle)¶
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schrodinger.application.glide.xpdes.
m_glide_XPviz_penal_blkpchg
(cthandle)¶
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schrodinger.application.glide.xpdes.
m_glide_XPviz_water_ligand
(cthandle)¶
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schrodinger.application.glide.xpdes.
m_glide_XPviz_penal_polar
(cthandle)¶
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schrodinger.application.glide.xpdes.
m_glide_XPviz_water_protein
(cthandle)¶
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schrodinger.application.glide.xpdes.
m_glide_XPviz_penal_ddpen
(cthandle)¶
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schrodinger.application.glide.xpdes.
m_glide_XPviz_penal_twistam
(cthandle)¶
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schrodinger.application.glide.xpdes.
m_glide_XPviz_penal_charge
(cthandle)¶
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schrodinger.application.glide.xpdes.
m_glide_XPviz_penalties
(cthandle)¶
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schrodinger.application.glide.xpdes.
m_glide_XPviz_picat
(cthandle)¶
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class
schrodinger.application.glide.xpdes.
TermKeywords
¶ Bases:
str
,enum.Enum
XP-descriptor term keywords. Note that members of this enum may be compared to bare strings.
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Molecule
= 'Molecule'¶
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H_bonds
= 'H_bonds'¶
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Phob_pack
= 'Phob_pack'¶
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Hex_pairs
= 'Hex_pairs'¶
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Penalties
= 'Penalties'¶
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Phobcon_HB
= 'Phobcon_HB'¶
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Picat
= 'Picat'¶
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Exposure
= 'Exposure'¶
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Rot_bonds
= 'Rot_bonds'¶
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Hex_sp
= 'Hex_sp'¶
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__class__
¶ alias of
enum.EnumMeta
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__members__
= mappingproxy(OrderedDict([('Molecule', <TermKeywords.Molecule: 'Molecule'>), ('H_bonds', <TermKeywords.H_bonds: 'H_bonds'>), ('Phob_pack', <TermKeywords.Phob_pack: 'Phob_pack'>), ('Hex_pairs', <TermKeywords.Hex_pairs: 'Hex_pairs'>), ('Penalties', <TermKeywords.Penalties: 'Penalties'>), ('Phobcon_HB', <TermKeywords.Phobcon_HB: 'Phobcon_HB'>), ('Picat', <TermKeywords.Picat: 'Picat'>), ('Exposure', <TermKeywords.Exposure: 'Exposure'>), ('Rot_bonds', <TermKeywords.Rot_bonds: 'Rot_bonds'>), ('Hex_sp', <TermKeywords.Hex_sp: 'Hex_sp'>)]))¶
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__module__
= 'schrodinger.application.glide.xpdes'¶
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class
schrodinger.application.glide.xpdes.
XpPVParser
(filename)¶ Bases:
object
Class for parsing a PV file with XP-descriptor information
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__init__
(filename)¶ Read PV file and create a table of XP Descriptor terms
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parseBlock_SL
(ctnum)¶ XP parsing for single-ligand scoring. Given ctnum, get and parse XP block return an array of tuples. tuple[0] is an atom number and tuple[1] is the corresponding XP score for that atom Added: tuple[2] the energy type e.g. r_xpdes_HBond which will be later set as an atom-level property.
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parseBlock_F
(ctnum, st)¶ XP parsing for fragment scoring. Use st argument to determine the number of rings associated with a set of atoms. Given ctnum, get and parse XP block return an array of tuples containing energy type e.g. r_xpdes_HBond which will be later set as an atom-level property.
Each entry = (atom number, XP score, energy type property)
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__class__
¶ alias of
builtins.type
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__delattr__
¶ Implement delattr(self, name).
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__dict__
= mappingproxy({'__module__': 'schrodinger.application.glide.xpdes', '__doc__': '\n Class for parsing a PV file with XP-descriptor information\n ', '__init__': <function XpPVParser.__init__>, 'parseBlock_SL': <function XpPVParser.parseBlock_SL>, 'parseBlock_F': <function XpPVParser.parseBlock_F>, '__dict__': <attribute '__dict__' of 'XpPVParser' objects>, '__weakref__': <attribute '__weakref__' of 'XpPVParser' objects>})¶
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__dir__
() → list¶ default dir() implementation
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__eq__
¶ Return self==value.
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__format__
()¶ default object formatter
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__ge__
¶ Return self>=value.
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__getattribute__
¶ Return getattr(self, name).
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__gt__
¶ Return self>value.
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__hash__
¶ Return hash(self).
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__init_subclass__
()¶ This method is called when a class is subclassed.
The default implementation does nothing. It may be overridden to extend subclasses.
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__le__
¶ Return self<=value.
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__lt__
¶ Return self<value.
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__module__
= 'schrodinger.application.glide.xpdes'¶
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__ne__
¶ Return self!=value.
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__new__
()¶ Create and return a new object. See help(type) for accurate signature.
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__reduce__
()¶ helper for pickle
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__reduce_ex__
()¶ helper for pickle
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__repr__
¶ Return repr(self).
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__setattr__
¶ Implement setattr(self, name, value).
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__sizeof__
() → int¶ size of object in memory, in bytes
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__str__
¶ Return str(self).
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__subclasshook__
()¶ Abstract classes can override this to customize issubclass().
This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).
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__weakref__
¶ list of weak references to the object (if defined)
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